Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH |
| |
Institution: | 1. Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mu′tah University, Alkarak Jordan;2. Department of Pharmaceutical Chemistry and Pharmacognacy, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan;3. Drug Discovery Unit, Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan;1. Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, International Campus, Mashhad, Iran;2. Computational Chemistry Research Lab., Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran;1. Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium;1. College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, PR China;2. Department of Physics, Pukyong National University, Busan 608-737, Republic of Korea |
| |
Abstract: | Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues – ASN14, THR18 and GLN44 – involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications. |
| |
Keywords: | Molecular dynamics Amber Antifreeze protein Water solvation |
本文献已被 ScienceDirect 等数据库收录! |
|